CHEMLINE: a Chemical Structure Search Key to Biological Information

1978 ◽  
pp. 58-72
Author(s):  
MELVIN L. SPANN ◽  
DONALD J. HUMMEL ◽  
ROBERT J. SCHULTHEISZ ◽  
SHARON L. VALLEY ◽  
DONALD F. WALKER
Keyword(s):  
Chemical Structure ◽  
Biological Information ◽  
Structure Search

scholarly journals Identification of new superwarfarin-type rodenticides by structural similarity. The docking of ligands on the vitamin K epoxide reductase enzyme’s active site

2015 ◽  
Vol 7 (1) ◽  
pp. 108-122
Author(s):  
László Ferencz ◽  
Daniela Lucia Muntean
Keyword(s):  
Vitamin K ◽  
Chemical Structure ◽  
Enzyme Inhibitors ◽  
Structural Similarity ◽  
Vitamin K Epoxide Reductase ◽  
Pubchem Compound ◽  
Structure Search ◽  
Epoxide Reductase ◽  
Compound Database ◽  
Similarity Thresholds

Abstract The rodenticide brodifacoum is highly toxic to mammals and birds, and extremely toxic to fish. It is a highly cumulative poison due to its high lipophilicity and extremely slow elimination. For this reason, it may be interesting to find similar compounds in order to enlarge the spectrum of vitamin K epoxide reductase enzyme inhibitors used today in pest control. We used the Similar Compounds search type of the Chemical Structure Search of the PubChem Compound Database to locate records that are similar to the chemical structure of brodifacoum, using pre-specified similarity thresholds. Using the threshold ≥ than 95% for the similar structures criteria, we found 14 compounds (from over 30 million entries) that meet this criteria. Two of these compounds have a better binding affinity to vitamin K epoxide reductase enzyme than brodifacoum, but the binding energy of the other 12 substances is also high, having identical or lower lipophilicity; consequently, they will eliminate faster, possibly lacking a part of the adverse effects.

scholarly journals Correction to: Interoperable chemical structure search service

2020 ◽  
Vol 12 (1) ◽  
Author(s):  
Miroslav Kratochvíl ◽  
Jiří Vondrášek ◽  
Jakub Galgonek
Keyword(s):  
Chemical Structure ◽  
Structure Search ◽  
Search Service

scholarly journals SIMCOMP/SUBCOMP: chemical structure search servers for network analyses

2010 ◽  
Vol 38 (Web Server) ◽  
pp. W652-W656 ◽  
Author(s):  
M. Hattori ◽  
N. Tanaka ◽  
M. Kanehisa ◽  
S. Goto
Keyword(s):  
Chemical Structure ◽  
Network Analyses ◽  
Structure Search

scholarly journals Inferring microRNA-Environmental Factor Interactions Based on Multiple Biological Information Fusion

Molecules ◽  
2018 ◽  
Vol 23 (10) ◽  
pp. 2439 ◽  
Author(s):  
Haiqiong Luo ◽  
Wei Lan ◽  
Qingfeng Chen ◽  
Zhiqiang Wang ◽  
Zhixian Liu ◽  
...  
Keyword(s):  
Information Fusion ◽  
Chemical Structure ◽  
State Of The Art ◽  
Anatomical Therapeutic Chemical ◽  
Computational Method ◽  
Biological Information ◽  
Mirna Sequence ◽  
Chemical Information ◽  
Factor Interactions ◽  
The Relationship

Accumulated studies have shown that environmental factors (EFs) can regulate the expression of microRNA (miRNA) which is closely associated with several diseases. Therefore, identifying miRNA-EF associations can facilitate the study of diseases. Recently, several computational methods have been proposed to explore miRNA-EF interactions. In this paper, a novel computational method, MEI-BRWMLL, is proposed to uncover the relationship between miRNA and EF. The similarities of miRNA-miRNA are calculated by using miRNA sequence, miRNA-EF interaction, and the similarities of EF-EF are calculated based on the anatomical therapeutic chemical information, chemical structure and miRNA-EF interaction. The similarity network fusion is used to fuse the similarity between miRNA and the similarity between EF, respectively. Further, the multiple-label learning and bi-random walk are employed to identify the association between miRNA and EF. The experimental results show that our method outperforms the state-of-the-art algorithms.

scholarly journals Interoperable chemical structure search service

2019 ◽  
Vol 11 (1) ◽  
Author(s):  
Miroslav Kratochvíl ◽  
Jiří Vondrášek ◽  
Jakub Galgonek
Keyword(s):  
Chemical Structure ◽  
Query Language ◽  
Search Space ◽  
Chemical Databases ◽  
Search Terms ◽  
Structure Search ◽  
Search Service ◽  
Large Databases ◽  
Similarity Searches ◽  
Small Molecule Databases

Abstract Motivation The existing connections between large databases of chemicals, proteins, metabolites and assays offer valuable resources for research in fields ranging from drug design to metabolomics. Transparent search across multiple databases provides a way to efficiently utilize these resources. To simplify such searches, many databases have adopted semantic technologies that allow interoperable querying of the datasets using SPARQL query language. However, the interoperable interfaces of the chemical databases still lack the functionality of structure-driven chemical search, which is a fundamental method of data discovery in the chemical search space. Results We present a SPARQL service that augments existing semantic services by making interoperable substructure and similarity searches in small-molecule databases possible. The service thus offers new possibilities for querying interoperable databases, and simplifies writing of heterogeneous queries that include chemical-structure search terms. Availability The service is freely available and accessible using a standard SPARQL endpoint interface. The service documentation and user-oriented demonstration interfaces that allow quick explorative querying of datasets are available at https://idsm.elixir-czech.cz.

Three-Dimensional Chemical Structure Search Using the Conformational Code for Organic Molecules (CCOM) Program

Chirality ◽  
2016 ◽  
Vol 28 (5) ◽  
pp. 370-375 ◽  
Author(s):  
Hiroshi Izumi ◽  
Laurence A. Nafie ◽  
Rina K. Dukor
Keyword(s):  
Chemical Structure ◽  
Organic Molecules ◽  
Three Dimensional ◽  
Structure Search

scholarly journals Analysis of Similarity/Dissimilarity of DNA Sequences Based on Chaos Game Representation

2013 ◽  
Vol 2013 ◽  
pp. 1-6 ◽  
Author(s):  
Wei Deng ◽  
Yihui Luan
Keyword(s):  
Dna Sequences ◽  
Chemical Structure ◽  
Globin Gene ◽  
Biological Information ◽  
Fractal Structures ◽  
Chaos Game Representation ◽  
Random Sequences ◽  
Analysis Of Similarity ◽  
Chaos Game ◽  
Game Representation

The Chaos Game is an algorithm that can allow one to produce pictures of fractal structures. Considering that the four bases A, G, C, and T of DNA sequences can be divided into three classes according to their chemical structure, we propose different kinds of CGR-walk sequences. Based on CGR coordinates of random sequences, we introduce some invariants for the DNA primary sequences. As an application, we can make the examination of similarity/dissimilarity among the first exon ofβ-globin gene of different species. The results indicate that our method is efficient and can get more biological information.

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